Session Start: Tue Dec 09 13:41:35 2008 Session Ident: #Chemistry [13:41] * Now talking in #Chemistry [13:41] * chemistry.gravitywaves.com sets mode: +nt [15:57] * curious has joined #Chemistry [16:01] * DrSturm has joined #Chemistry [16:01] * shrimp has joined #Chemistry [16:03] hello dr.strum,,what is the role of non-reducing sugars [16:04] Energy production, energy storage [16:06] how does the removal of phosphate group from ATP drive endergonic reactions [16:06] Breaking the phosphate bond is exothermic, releases energy [16:09] what is the total amount of ATP produced from one glucose , starting from glycolysis to electron transport chain [16:11] 24 out of the Citric acid cycle, 6 from the PDH and 2 from glycolysis so 32 [16:12] if one molecule of glucose goes through glycolysis then anaerobic metabolism, does it produce 4 ATP? [16:13] 2 [16:13] Do we have to know all the components of the electron transport chain starting with NADH DH to Cyta? [16:14] yes [16:14] * adeline has joined #Chemistry [16:14] do we need to know how the PDH complex works,,with TDP and lipoate,,producing acetyl coA,NADH,CO2 [16:15] PDH is the enzyme that converts Pyruvate, NAD+, CoASH into Acetyl CoA, NADH, CO2 and H+. Also know its regulation. [16:15] * Glycogen has joined #Chemistry [16:15] question: do we need to know details about the E1, E2, and E3 of the TCA cycle? [16:16] * shrimp has quit IRC (Quit: Leaving) [16:16] That is the PDH. PDH is the enzyme that converts Pyruvate, NAD+, CoASH into Acetyl CoA, NADH, CO2 and H+. Also know its regulation. [16:16] * shrimp has joined #Chemistry [16:17] * Guillom has joined #Chemistry [16:17] do you mean feedback inhibition? [16:17] What is allosteric regulation of Glycogen Synthase? [16:17] Yes, Feedback Inhibition: - Acetyl CoA and NADH [16:18] what are the enzymes of glutathione metablism? [16:18] * PPP has joined #Chemistry [16:19] Dr. Sturm can you identify the composition of the following disaccharides: alpha lactose, Beta Sucrose and B maltose? [16:19] Glutathione reductase and glutathione peroxidase [16:19] do we need to know any of the enzymes associated with glyconeogenesis [16:19] All of them [16:20] what is the function of DHAP? [16:20] lactose, sucrose and maltose are defined in the lecture notes [16:20] it is an intermediate in glycolysis [16:20] Do we need to any of the pathway's completely from top to bottom or should we focus on the areas where ATP/NAD etc is used and made including the enzymes involved and the product of the reaction? [16:20] What is allosteric regulation of Glycogen Synthase? [16:20] You need to know: Glycolysis (see hand-out); Citric Acid Cycle; Glycogenolysis; Glycogenesis; Gluconeogenesis (G-6-Pase and F-1,6-BPase reactions); Electron Transport Chain (see hand-out) [16:21] * kobby has joined #Chemistry [16:21] what is the definition of a futile cycle [16:21] Can you identify where specific biochemical processes occur in the cell? [16:21] Glycogen synthase is activated by G-6-P [16:22] Tx. [16:22] A futile cycle is a cycle (loop) where ATP is used but not regenerated. There could be futile cycles formed by Hexokinase (Glucokinase)/G-6-Pase and PFK/F-1,6-BPase in glycolysis/gluconeogenesis but they are stopped because of the strict regulation of the enzymes. [16:22] thanks [16:22] Check the Chemistry of Life/The Cell lecture notes [16:23] Do we need to know how many kcal/mol phosphate compounds produce? [16:23] Can you describe the significance of the adnylate Kinase reaction in metabolic regulation? [16:23] Dr. Strum WK sheet 22, Q 1. List the function of mitochondria....? Do we need to explain the details including the inner mitochondria membrane function? [16:23] Yes Kcals [16:24] Adenylate kinase catalyzs the conversion of ATP and AMP to ADP [16:24] In the lecture notes only alpha-maltose, alpha-sucrose, and beta-lactose are given while the worksheet askes for beta-maltose, beta -sucrose, and alpha-lactose. What would be there be a difference [16:24] ? [16:25] * kobby has quit IRC (Ping timeout: 240 seconds) [16:25] Can you differentiate b/ the isozymes of lactate dehydrogenase? [16:25] They have the composition, alpha or beta [16:25] Don't need to konw the isozymes of LDH [16:26] how much detail do we have to know abou the structure of the mitochondria? [16:26] Alpha/beta sugars have the same composition [16:26] Nothing about the structure of the mitochondria [16:27] Dr. Strum The three main function of PPP are Source of NADPH, Pentoses for Nuclic acid synthesis, and interconversion of pentoses with hexoses? [16:27] Can you list the general features of the steps in Glycogenolysis and glycogenesis? [16:27] Yes. [16:28] Check the lecture notes for the Glycolysis/Glycogenesis pathways [16:28] is the purpose of the mass action effect to produce lots of AMP [16:28] identify the 3 main function of the PPP [16:28] Not the purpose but because of the stoichiometry of 1 ATP and 1 AMP making 2 ADP it happens that way [16:29] PPP: Source of NADPH (reductive synthesis, maintainence of glutathione in the reduced state), pentoses for nucleic acid synthesis, interconversion of pentoses with hexoses and trioses [16:29] Do we need to know the steps and enzymes for Acetyl CoA or just about its regulation? [16:30] PDH is the enzyme that converts Pyruvate, NAD+, CoASH into Acetyl CoA, NADH, CO2 and H+. Also know its regulation (inhibited by Acetyl CoA and NADH). [16:30] Can you identify for me the enzyme of glutathione metabolism and relationship of this metabolism to the pentose pathway and protection of the cell against oxidants? [16:30] would the differentiation between alpha-sucrose and beta-sucrose be on Carbon 1 of the glucose pyranosyl ring and on Carbon 2 of the fructofuranoside ring or just one ring? [16:31] Dr. Strum, Is this right? Specific biochemical processes occurs - aerobic metabolism in mitochondria, and Anerobic is in RBC? [16:33] Alpha, beta comes from the -OH group on the anomeric "C" and whether it is up or down [16:33] are we responsible for specific activitys of precursors associated with gluconeogenesis,lactate,alanine,glycerol [16:33] Do we have to know for E1,E2, and E3 of the PDH what goes into the complex and what comes out [16:34] Glutathione oxidized is reduced by Glutathione Reductase. Glutathione in its reduced form removes H2O2 (peroxides) from the plasma preventing RBC membrane destruction and ultimately hemolytic anemia. [16:34] * adp has joined #Chemistry [16:34] You need to know there are non-CHO precursors to gluconeogenesis, that's all [16:34] PDH is the enzyme that converts Pyruvate, NAD+, CoASH into Acetyl CoA, NADH, CO2 and H+. Also know its regulation (inhibited by Acetyl CoA and NADH). [16:35] Do we need to know the steps/diagram of the regulation of glycogenolysis or glycogenesis? [16:35] Aerobic metabolism requires mitochondria, anaerobic metabolism is not restricted to RBC's though it does occur in RBC's [16:36] Glycogen Phosphorylase: Activator: AMP; Inhibitor: ATP, glucose, glucose-6-phosphate; Glycogen Synthase: Activated by G-6-P [16:38] Can you identify the enzymes, substrates and product of the glycolytic pathway? [16:39] See the Hand-out from lecture [16:39] Meeting cellular needs: should we know the all non-oxidative and oxidative branches ans what happens? [16:39] No [16:40] Can you describe the significance of the adenylate kinase reaction in metabolic regulation? [16:41] just to clear things up, for alpha-maltose there are two anomeric carbons and both are down, would beta make both of them up? [16:41] do we have to know glycogenesis? [16:42] Only the -OH group on the anomeric carbon involved in the glycosidic bond matters in the alpha, beta designation in the name [16:42] Yes, glycogenesis [16:42] Glycolysis (see hand-out); Citric Acid Cycle; Glycogenolysis; Glycogenesis; Gluconeogenesis (G-6-Pase and F-1,6-BPase reactions); Electron Transport Chain (see hand-out) [16:42] Do we have to know the Metabolic terms? [16:42] No [16:43] Just to check you also said we don't have toknow the nine types of Metabolic regulations [16:44] Correct [16:44] Do we need to read the detailed notes for Electron transport or Just the Hand out that you gave us the last of Lecture. [16:44] Hand-out [16:44] * kobby has joined #Chemistry [16:44] Are we going to be responsible for knowing how many ATP/NADH etc are made and used throughout each cycle? [16:44] Yes [16:45] do we have to know the substrate level phosphorylation vs oxidative phosphorylation? [16:45] Yes. [16:45] What should we focus on for the ATP Synthase Complex? [16:46] It is not on the hand-out so nothing [16:47] Thank you [16:47] In pyruvate Kinase and energy yield do we have to know how many ATP is produced? [16:47] * glycogen1 has joined #Chemistry [16:47] * glycogen1 has quit IRC (Quit: Leaving) [16:47] Dr. Strum just to confirm, 2 ATP produced for glycogenesis ? [16:47] Don't understand in "Pyruvate Kinase"? [16:47] * PPP1 has joined #Chemistry [16:48] * ET has joined #Chemistry [16:48] 2 ATP per one glucose, galactose or fructose in glycolysis [16:48] will we have to draw out the pathways on the exam? [16:48] You need to know these pathways: Glycolysis (see hand-out); Citric Acid Cycle; Glycogenolysis; Glycogenesis; Gluconeogenesis (G-6-Pase and F-1,6-BPase reactions); Electron Transport Chain (see hand-out) [16:49] How many ATP for glycogen Synthesis ? 4 because 2 per Glucose? [16:49] * PPP1 has quit IRC (Quit: Leaving) [16:49] We didn't talk about energy production with respect to the glycogen pathways [16:49] in the electron transport chain,each of the 3 sites produce 2 H+,how does it produce ATP [16:49] Thanks [16:50] * Biochem has joined #Chemistry [16:50] The positive charges of the H+ change the gradient across the inner mitochondrial membrane driving the pump [16:50] * PPP has quit IRC (Quit: Leaving) [16:51] are the isoenzymes of lactate dehydrogenase required for the exam? [16:51] No. [16:52] which pathways will we have to know the energy prod. of? [16:53] Glycolysis, PDH, Citric acid cycle and how they relate to the electron transport chain, i.e. how we get ATP from NADH/FADH2 [16:56] Dr. Strum Is this right Ans. for Above Question, that electrons require to ATp synthesis, and Electron carriers FADH, NADPH are transported through Elecron Transport chain. [16:58] Electrons from the NADH/FADH2 produced in the Citric Acid Cycle enter the electron transport chain where they produce protons which drive a pump that produces ATP [16:58] Tx [16:59] * shrimp has quit IRC (Quit: Leaving) [17:00] how do the g-6-p pathways connect with the citric acid cycle and electron transport chain? [17:01] oxidative and non-oxidative branch, do we need to know? [17:01] what are the G-6-P pathways? [17:01] Don't need to know oxidative vs non-oxidative branches [17:01] glyocolysis, glycogenolysis, gluconeogenesis [17:03] Glycolysis produces Pyruvate, Glycogenolysis produces G-6-P which enters glycolysis, the pyruvate goes through the PDH and into the citric acid cycle as Acetyl CoA [17:03] Gluconeogenesis also produces G-6-P which can enter glycolysis [17:05] what should we know about the pp pathway? [17:06] PPP: Source of NADPH (reductive synthesis, maintainence of glutathione in the reduced state), pentoses for nucleic acid synthesis, interconversion of pentoses with hexoses and trioses [17:07] what should we know about glutathione? [17:07] Glutathione oxidized is reduced by Glutathione Reductase. Glutathione in its reduced form removes H2O2 (peroxides) from the plasma preventing RBC membrane destruction and ultimately hemolytic anemia. [17:09] what will we need to know about adenylate kinase [17:10] Adenylate kinase is an enzyme that catalyzes the conversion of ATP and AMP to ADP [17:11] * G-6-P has joined #Chemistry [17:11] Can you list the general features and function of ATP? [17:12] See the lecture notes on Thermodynamics of Metabolism [17:14] phosphocreatine, 1,3-BPG and PEP drive endergonic rxns, correct? [17:14] Yes. [17:14] the glutathione reduring lecture you told us to cross out gluconeogenesis and earlier you mentioned that we have to know, do we or no? [17:15] Gluconeogenesis (G-6-Pase and F-1,6-BPase reactions) [17:15] Also: A futile cycle is a cycle (loop) where ATP is used but not regenerated. There could be futile cycles formed by Hexokinase (Glucokinase)/G-6-Pase and PFK/F-1,6-BPase in glycolysis/gluconeogenesis but they are stopped because of the strict regulation of the enzymes. [17:16] Would you say a good bulk of the exam will come from the information asked on the handouts? [17:16] In worksheet 20 question 2 in the thermodynamic in metabolism, do we have to know the definition of high energy phosphate transfer potential and identify ATP, Phophocreatine, 1,3-BpG....? [17:16] It is pretty equally distributed over all of the topics [17:17] Yes [17:18] What do you mean by identify ATP, phosphocreatine, 1,3-BPG and phospoenolpyruvate as high energy phosphorylated compounds? [17:19] * ET has quit IRC (Quit: Leaving) [17:19] * ET has joined #Chemistry [17:20] do you mena where ATP is synthesized using the energy produced by the reduction of oxygen to water in mitochandria [17:20] Know the Kcals they produce [17:20] Is there going to be a crossword puzzle on the exam? [17:20] No [17:21] How about some happy holiday extra credit? :) [17:21] the exam is going to have multiple choice, T/F and short answers? [17:22] Afraid not... [17:22] Yes, MC, T/F and short answer [17:22] Do we have to know the cofactor of glycogen phosphorylase? [17:22] Is there anyway we could know how many MC, and T/F? [17:22] No [17:23] which kcals do we have to know? [17:23] 8 of 29 questions are MC or T/F [17:23] Do we have to know the active and inactive forms of glycogen phosphorylase and glycogen synthase? [17:24] Kcals for 1,3-BPG, phosphocreatine, PEP and ATP [17:24] No just: Glycogen Phosphorylase: Activator: AMP; Inhibitor: ATP, glucose, glucose-6-phosphate; Glycogen Synthase: Activated by G-6-P [17:25] there is a lot of information for this exam, is there a way that you could sum up the major points that will be covered? [17:25] For the ATP the kcal are -7.3, and -6.6 is that wright? [17:26] I tried to do that as we moved through the material so check your class notes [17:26] Yes for ATP [17:27] why are there two kcals for atp? [17:27] can we say just -13.9 for ATP or we have to separate them for each of the phosphates? [17:28] * biochem1 has joined #Chemistry [17:28] gamma/beta vs alpha/beta bonds [17:28] Depends on the question asked.\ [17:28] what section in the notes is the info about kcals? [17:29] for the elcetron transport system, would say to focus on the purple handout? [17:29] Yes. [17:29] Do we have to memorize the definiton for the two types of phosphorylations [17:29] what section in the notes has the info about kcals? [17:30] do we have to know the information on mitochondria for the test? [17:30] the handout or the worksheet? [17:30] Intro to Metabolism, "High Energy Phosphate Bonds" [17:30] Electron Transport, hand-out [17:31] Depends what you mean by "information on mitochondria"? [17:31] the structure and function [17:31] structures* [17:31] Don't need to know [17:32] Do we have to know the definition of the two types of phosphorylation? [17:32] Yes [17:32] how about the energy production numbers? (citric acid lecture) [17:32] Yes [17:33] Do we have to know about laChatlier principle? [17:33] No [17:34] do we need to know where the energy of atp is stored? the phosphoanhydride bonds [17:34] we do not have to know about free energy section? [17:34] Yes and Yes [17:35] do we need to know the citric acid cycle where the nadh's are formed and the fadh2 [17:36] Yes [17:36] Glycolysis (see hand-out); Citric Acid Cycle; Glycogenolysis; Glycogenesis; Gluconeogenesis (G-6-Pase and F-1,6-BPase reactions); Electron Transport Chain (see hand-out) [17:36] * G-6-P has quit IRC (Quit: Leaving) [17:36] will we be drawing out the pathways themselves? or will we just be asked questions about the details? [17:36] Both are possible [17:37] there will be 29 questions, right? [17:37] Yes. [17:38] how about the specific subrates (glycogen Pi) cofactor of glycogen phosph [17:38] No [17:39] will we need to know both the functions and metabolic processes of the mitochondria? [17:39] No [17:39] where doe wsteh DNP activate the e- transport chain [17:40] DNP causes consumption of oxygen without porducing ATP, aka uncoupling [17:40] will we need to know the sources and fates of pyruvate and acetyl CoA? [17:40] do we need the inorganic pi/O2 ratio? [17:41] No [17:41] ATPase complex? [17:41] Yes P/O ratio which is 3 for NADH and 2 for FADH2 [17:41] ATPase complex is not on the hand-out [17:42] will we need to know the prods of complete oxidation of pyruvate? [17:42] as far as the gluconeogenic precursors, do we just gotta know what they are? or do we have to be able to give their products and enzymes [17:42] Do we have to know the energy production of NADH in alpha-glycerol phosphate shuttle and malate-aspartate shuttle? [17:43] Just that there are non-CHO gluconeogenic precursors [17:43] No shuttles [17:43] uncoupling and oligomycin [17:44] They are on the hand-out so yes [17:44] f1, stalk, and f0? [17:45] Are they on the hand-out? [17:45] yeah as part of the ATPase synthase complex [17:46] what is the biochemical basis of fructose intolerance? [17:46] If they are on the lilac hand-out given in class then they are important [17:47] * kobby has quit IRC (Ping timeout: 240 seconds) [17:47] A defect in one of the enzymes in the fructose part of the glycolysis pathway [17:47] treatment?? [17:47] do we have to know the isozymes H4 and M4 and what they're inhibited by etc? [17:47] No [17:48] what is the treatment for the disorder? [17:48] Don't eat fructose [17:48] ok [17:48] as far as a definition for a reducing sugar, would this be correct...the free o on the anomeric carbon [17:49] Do we have to know detailes of PEPCK and Pyruvate Carboxylase? [17:49] For gluconeogenesis: Gluconeogenesis (G-6-Pase and F-1,6-BPase reactions) [17:50] * Guillom has quit IRC (Quit: Leaving) [17:50] What do we have to know about free energy? Just Adenylate kinase? [17:50] If the -OH attached to the anomeric "C" is free, i.e. not attached to anything, the sugar is a reducing sugar [17:50] will we need to know about the cori and glucose-alanine cycles? [17:51] So only the part that you gave us the gluconeogenesis starts from g-1,6bp only? [17:51] Gluconeogenesis (G-6-Pase and F-1,6-BPase reactions) [17:51] All of the inofrmation under "Free Energy" is important except the equations [17:52] will we have to ID gluconeogenic precursors, products and enzymes? [17:52] * G-6-P has joined #Chemistry [17:53] Just that there are non-carbohydrate gluconeogenic precursors. [17:53] * G-6-P has quit IRC (Quit: Leaving) [17:54] in glycogenesis, do we need to know glycogen synthase i and glycogen synthase d [17:54] No [17:55] * curious has quit IRC (Read error: Connection reset by peer) [17:56] how about the pathway of glycogenolysis? or do we just need to know the key enzyme and its regulation [17:56] Need to know the pathway and regulation of the phosphorylase [17:57] Any last questions? [17:57] not from me......thanks [17:57] thanks [17:57] You are welcome. [17:57] * biochem1 has quit IRC (Quit: Leaving) [17:58] Thank you [17:58] You're welcome [17:58] * DrSturm has quit IRC [17:59] * Disconnected Session Close: Tue Dec 09 17:59:09 2008